Long wavelength and near infrared (NIR) dyes have been shown to act as excellent reporter components in targeting molecular probes and tracers. Many of the currently available fluorescent dyes and probes have undesirable properties such as relatively high non-specific protein binding and a tendency to aggregate and are prohibitively expensive due in part to unoptimized synthetic methods. The main focus of this work is to discover novel, water soluble, long wavelength near-infrared cyanine dyes that are designed for use in high throughput screening, imaging and other applicable techniques such as immunofluorescence microscopy, fluorescence resonance energy transfer and fluorescence activated cell sorting and counting. Novel synthetic solution and solid phase chemistry pathways will be developed that will allow gram-scale synthesis of the dyes in high purity and will result in better products that will be more widely available at lower cost to the research and scientific community. There are 10 specific aims: (1) To Prepare a Combinatorial Chemistry Library of 120 New Benzocrown-ether Long Wavelength Cyanine Dyes Using the Synthetic Methodologies Developed in Phase I. (2) To Prepare a Combinatorial Chemistry Library of 180 New Polyethylene Glycol Long Wavelength Cyanine Dyes Using the Synthetic Methodologies Developed in Phase I. (3) Purification and Characterization of the New Dyes. (4) Dye Stability and Solubility Studies. (5) Non-Specific Binding Studies. (6) Scale up Synthesis of 15 Selected Cyanine Dyes. (7) Fluorescence Polarization (FP) Studies. (8) To Assess the Performance of the New Dyes in Fluorescence Resonance Energy Transfer (FRET) Studies. (9) Immunohistochemical Studies with the New Dyes. (10) Synthesis of Alternate Reactive Handles. [unreadable] [unreadable]